ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.

AuthorPeter Humburg
Date of publicationNone
MaintainerPeter Humburg <peter.humburg@gmail.com>
LicenseGPL (>= 2)
Version1.28.0

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Man pages

accessors: Access slots of S4 classes

alignFeature: Read counts relative to annotated features

BindScore: Class "BindScore"

callBindingSites: Predict protein binding sites from high-throughput sequencing...

ChIPseqR-package: Identifying Protein Binding Sites in High-Throughput...

compress-BindScore: Compress BindScore Objects

compress-methods: Methods for Function compress in Package 'ChIPseqR'

compress-ReadCounts: Compress ReadCount Objects

decompress: Extract Read Count and Binding Site Score Representations

decompress-methods: Methods for Function decompress in Package 'ChIPseqR'

exportBindSequence: Export sequence of predicted binding sites

getBindCor: Calculate cross-correlation between read counts

getBindLen: Estimate length of binding and support region

getCutoff: Determine significance threshold for binding site scores

internal: Internal and undocumented functions

pickPeak: Identify peaks above a given threshold

plot-BindScore: Diagnostic Plots for Binding Site Scores

plot-ReadCounts: Diagnostic Plots for Read Counts

plotReads: Plot compact representation of read counts on a chromosome

plotWindow: Plot read counts within a genomic region

pos2gff: Convert genome coordinates into GFF format

ReadCounts: Class "ReadCounts"

RLEBindScore-class: Run-length Encoded Binding Site Scores

RLEReadCounts-class: Run-length Encoded Read Counts

simpleNucCall: Predict nucleosome positions from high-throughput sequencing...

startScore: Score potential protein binding sites

strandPileup: Strand specific read counts

windowCounts: Summarize read counts in a sliding window

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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